Abstract In West Africa, the use of organophospates and pyrethroid insecticides to control cotton pests has led to the evolution of resistance in field populations of Bemisia tabaci Gennadius. Three pest management programs have been commonly recommended: the Conventional Program (CP) where 6 treatments are applied, the use of Bt cotton plants for which only 2 applications of neonicotinoids are required and that has been adopted in many countries, and a biological program (BP) without any chemical treatment. The present study aimed to determine the influence of these practices on the frequency of mutations that confer resistance to pyrethroids (mutation L925I in the para-type voltage-gated sodium channel gene) and organophosphates (mutation F331W in the acetylcholinesterase enzyme ace1: allele Ace1 R) in B. tabaci populations using Bt cotton and CP areas in Pô and Saria …